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&#160;

<h3><a id="index_a"></a>- a -</h3><ul>
<li>add_alignment()
: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#adc32085da2b5681f0045d05c43a35f92">claragenomics::cudaaligner::Aligner</a>
</li>
<li>add_edge()
: <a class="el" href="classclaragenomics_1_1DirectedGraph.html#a85c21aed5db9c7d81cb6003841410371">claragenomics::DirectedGraph</a>
, <a class="el" href="classclaragenomics_1_1UndirectedGraph.html#a47c5ee6b9616ab24222526f4dcd1fb04">claragenomics::UndirectedGraph</a>
</li>
<li>add_poa_group()
: <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a8f2f44e7b4d7f51d8ba68323841dcdf0">claragenomics::cudapoa::Batch</a>
</li>
<li>align_all()
: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a8b3c20782b9eaa4c2219fb7ff51772db">claragenomics::cudaaligner::Aligner</a>
</li>
<li>Anchor()
: <a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html#af4dc10f114030a8e3a53f3bad3cd20b2">claragenomics::cudamapper::Anchor</a>
</li>
<li>anchors()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac3de5ba06b0c7ef0329caf71ae98f2d2">claragenomics::cudamapper::Matcher</a>
</li>
</ul>


<h3><a id="index_b"></a>- b -</h3><ul>
<li>batch_id()
: <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab807c4b01c2cddcdebb32952df13c0ec">claragenomics::cudapoa::Batch</a>
</li>
</ul>


<h3><a id="index_c"></a>- c -</h3><ul>
<li>convert_to_cigar()
: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#aeb4a583f6fbc643c93170797ca45a876">claragenomics::cudaaligner::Alignment</a>
</li>
<li>create_index()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a47c3cb89daa4076243dd5977acfb7ccf">claragenomics::cudamapper::Index</a>
</li>
<li>create_matcher()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ae65a1507ddf1bf2aa046fc0eacfea752">claragenomics::cudamapper::Matcher</a>
</li>
<li>create_sequence()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html#a3e4a8fe41b71b13362433360b20115ed">claragenomics::cudamapper::Sequence</a>
</li>
</ul>


<h3><a id="index_d"></a>- d -</h3><ul>
<li>data()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html#a45c1a69a18ea6f6fd7a45bad6862bbca">claragenomics::cudamapper::Sequence</a>
</li>
<li>directed_edge_exists()
: <a class="el" href="classclaragenomics_1_1Graph.html#a1df5a4be1fc2f71130436e9f718e85ac">claragenomics::Graph</a>
</li>
<li>direction()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#af4b53bc09f5816c3b81fef1c1abf3fc6">claragenomics::cudamapper::SketchElement</a>
</li>
<li>directions_of_reads()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5824f352fd89f69c9acc14430a3aa6cd">claragenomics::cudamapper::Index</a>
</li>
</ul>


<h3><a id="index_e"></a>- e -</h3><ul>
<li>edges_to_dot()
: <a class="el" href="classclaragenomics_1_1Graph.html#a88dda0ee0cffa26a188a041593d2fcd5">claragenomics::Graph</a>
</li>
</ul>


<h3><a id="index_f"></a>- f -</h3><ul>
<li>filter_overlaps()
: <a class="el" href="group__cudamapper.html#ga3e5732f34489315ec8d1ef8b82ccea5c">claragenomics::cudamapper::Overlapper</a>
</li>
<li>first_occurrence_of_representations()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af4f69a9003fedb9ca11665d5faa43bff">claragenomics::cudamapper::Index</a>
</li>
<li>format_alignment()
: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4be4bb544d593f3fd7624628f2bda29c">claragenomics::cudaaligner::Alignment</a>
</li>
</ul>


<h3><a id="index_g"></a>- g -</h3><ul>
<li>generate_poa()
: <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a7387b746531d4e8ac1e5806ac2824f09">claragenomics::cudapoa::Batch</a>
</li>
<li>get_adjacent_nodes()
: <a class="el" href="classclaragenomics_1_1Graph.html#ab52b2707de415931f1990ee338b29eeb">claragenomics::Graph</a>
</li>
<li>get_alignment()
: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a5139f26517193e077000dcddfbc15f70">claragenomics::cudaaligner::Alignment</a>
</li>
<li>get_alignment_type()
: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab22457c02ac00ec205dcd5a75b253881">claragenomics::cudaaligner::Alignment</a>
</li>
<li>get_alignments()
: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a1d775f9821ce3ecdcdc67cb07f35a4d8">claragenomics::cudaaligner::Aligner</a>
</li>
<li>get_consensus()
: <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a3224d1595caa5950c34708f4b7d64fe0">claragenomics::cudapoa::Batch</a>
</li>
<li>get_edges()
: <a class="el" href="classclaragenomics_1_1Graph.html#ac96335c01273c0dd74d2628e7bf38794">claragenomics::Graph</a>
</li>
<li>get_graphs()
: <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a0949cca1e89a40d759b0ca371512bb16">claragenomics::cudapoa::Batch</a>
</li>
<li>get_msa()
: <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab39956c82d5d5a2d8df1b1695e15d9d2">claragenomics::cudapoa::Batch</a>
</li>
<li>get_node_ids()
: <a class="el" href="classclaragenomics_1_1Graph.html#a1b51bca4b58c9922b375c983415ec0c8">claragenomics::Graph</a>
</li>
<li>get_node_label()
: <a class="el" href="classclaragenomics_1_1Graph.html#a47bd2f14a355fbbd801846b0af305389">claragenomics::Graph</a>
</li>
<li>get_num_seqences()
: <a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html#a04f6deee5108374fa485487e06e759e5">claragenomics::io::FastaParser</a>
</li>
<li>get_overlaps()
: <a class="el" href="group__cudamapper.html#gab0e3be4a9442dfb2b7952fb473e591a3">claragenomics::cudamapper::Overlapper</a>
</li>
<li>get_query_sequence()
: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab29dceafccd3cb0a2e87023c5d48a780">claragenomics::cudaaligner::Alignment</a>
</li>
<li>get_sequence_by_id()
: <a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html#a04a44819b81a93711295198492cc3765">claragenomics::io::FastaParser</a>
</li>
<li>get_sequence_by_name()
: <a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html#ad37d794106d347d1d360d62db2d31cda">claragenomics::io::FastaParser</a>
</li>
<li>get_status()
: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a7665f284b7929998357c89461e444f78">claragenomics::cudaaligner::Alignment</a>
</li>
<li>get_target_sequence()
: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4a61cdee74c32930f49cb878fc17db57">claragenomics::cudaaligner::Alignment</a>
</li>
<li>get_total_poas()
: <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#af2b27869811283b869700c181a75cfdc">claragenomics::cudapoa::Batch</a>
</li>
</ul>


<h3><a id="index_m"></a>- m -</h3><ul>
<li>maximum_kmer_size()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919">claragenomics::cudamapper::Index</a>
</li>
</ul>


<h3><a id="index_n"></a>- n -</h3><ul>
<li>name()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html#ab9663611f0d6c691e40228c5a08cf0e2">claragenomics::cudamapper::Sequence</a>
</li>
<li>node_labels_to_dot()
: <a class="el" href="classclaragenomics_1_1Graph.html#a95ef438f6035c2240bf277645ad27cb9">claragenomics::Graph</a>
</li>
<li>number_of_reads()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac9e936ae3809c82894a22a5ddb6bb937">claragenomics::cudamapper::Index</a>
</li>
</ul>


<h3><a id="index_o"></a>- o -</h3><ul>
<li>operator()()
: <a class="el" href="structclaragenomics_1_1PairHash.html#a46da7ce33ff4cf8a586a0c54b6be1e61">claragenomics::PairHash</a>
</li>
</ul>


<h3><a id="index_p"></a>- p -</h3><ul>
<li>position_in_read()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a0ddea36eed82ea3a9d1fa7ace61051bc">claragenomics::cudamapper::SketchElement</a>
</li>
<li>positions_in_reads()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a66e5d024befc410221610f454eff7183">claragenomics::cudamapper::Index</a>
</li>
<li>print_paf()
: <a class="el" href="group__cudamapper.html#ga54fedd97206ad1691f7b9d9966d01371">claragenomics::cudamapper::Overlapper</a>
</li>
</ul>


<h3><a id="index_r"></a>- r -</h3><ul>
<li>read_id()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#af5f2e8fc8df725b336833930baf3cd39">claragenomics::cudamapper::SketchElement</a>
</li>
<li>read_id_to_read_length()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a59186cdd6dbfd21baeb07e80bd4354d4">claragenomics::cudamapper::Index</a>
</li>
<li>read_id_to_read_name()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac59d309eeb226592a96622fec2b307fd">claragenomics::cudamapper::Index</a>
</li>
<li>read_ids()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5cfe03b47850170ec64d61d2dbef0401">claragenomics::cudamapper::Index</a>
</li>
<li>representation()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#abb3c8927594ba5f077c4443c229e0730">claragenomics::cudamapper::SketchElement</a>
</li>
<li>representations()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a876d5e82f9fc36f481854f7d84e5fc80">claragenomics::cudamapper::Index</a>
</li>
<li>reset()
: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a9f7f056a269c32c909a9bfb7132ba439">claragenomics::cudaaligner::Aligner</a>
, <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#aa8de262cb7c43d7219f7064bb700e7ae">claragenomics::cudapoa::Batch</a>
</li>
</ul>


<h3><a id="index_s"></a>- s -</h3><ul>
<li>scoped_device_switch()
: <a class="el" href="classclaragenomics_1_1scoped__device__switch.html#a41381ff64aeb0750803a315020a13650">claragenomics::scoped_device_switch</a>
</li>
<li>serialize_to_dot()
: <a class="el" href="classclaragenomics_1_1DirectedGraph.html#a7844605760f22a2a60e27c23178497b3">claragenomics::DirectedGraph</a>
, <a class="el" href="classclaragenomics_1_1UndirectedGraph.html#a64b119c6ca6049b081ddde7db3c87e3f">claragenomics::UndirectedGraph</a>
</li>
<li>set_node_label()
: <a class="el" href="classclaragenomics_1_1Graph.html#a9861d50dbee863befed15eb8daacff3d">claragenomics::Graph</a>
</li>
<li>sync_alignments()
: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#ac929b7ba836dfac74d8975f652563482">claragenomics::cudaaligner::Aligner</a>
</li>
</ul>


<h3><a id="index_u"></a>- u -</h3><ul>
<li>unique_representations()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a">claragenomics::cudamapper::Index</a>
</li>
<li>update_adject_nodes()
: <a class="el" href="classclaragenomics_1_1Graph.html#a0043ec8f35f7491c06915c887d31ea77">claragenomics::Graph</a>
</li>
</ul>


<h3><a id="index__7E"></a>- ~ -</h3><ul>
<li>~Aligner()
: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#aaae329eae2ed3e364db643163755e987">claragenomics::cudaaligner::Aligner</a>
</li>
<li>~Alignment()
: <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a6479df67f21d643782abfed873218ea8">claragenomics::cudaaligner::Alignment</a>
</li>
<li>~Batch()
: <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab70c94f0a2b161abd8fce03f487c2db1">claragenomics::cudapoa::Batch</a>
</li>
<li>~FastaParser()
: <a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html#a213af5341107ea254176add6dd1dfd2d">claragenomics::io::FastaParser</a>
</li>
<li>~Index()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#afcaccc9f9526d9c66280eca17ff3a4ac">claragenomics::cudamapper::Index</a>
</li>
<li>~Matcher()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html#ac2f70fb6b1876d0fa81fd8c0189191ab">claragenomics::cudamapper::Matcher</a>
</li>
<li>~Overlapper()
: <a class="el" href="group__cudamapper.html#ga569c8855bdf9806d3747b26fc7e98975">claragenomics::cudamapper::Overlapper</a>
</li>
<li>~scoped_device_switch()
: <a class="el" href="classclaragenomics_1_1scoped__device__switch.html#ad17a140b9fc9badff82487e685013125">claragenomics::scoped_device_switch</a>
</li>
<li>~Sequence()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html#a11498adb0025e53f3e397f72decc4e4f">claragenomics::cudamapper::Sequence</a>
</li>
<li>~SketchElement()
: <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#ac62560de124742cb23bc1def0a0b2069">claragenomics::cudamapper::SketchElement</a>
</li>
</ul>
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